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Being interrupted by three mysterious shadows in the middle of their combat against Groudon, Wallace demands to know who the intruders are, and the three reveal themselves to be the FireHeads Trio of Team Magma. Hank grins that the only means to dry up the sea and expand the land is to have Groudon unleash its powers across the entire Hoenn region, and that no one is allowed to interfere with their team’s grand scheme. Without another word, the FireHeads lift themselves into the air on their Swellows, and plunge towards the astounded gymleaders. Tabitha grabs Wallace by his neck to yank him off the ground, while Hank takes Brawly by the ankle, and Courtney pulls Roxanne up by the collar.

Forcing the gymleaders away from Groudon, the Team Magma admins hover over to Lilycove City, and each picks a separate battle ground to fight their chosen opponent. Brawly gets thrown hard onto the ground by Hank, and finds himself inside the Lilycove Museum. Wallace is taken to the Lilycove Department Store, while Roxanne lands in the severely damaged Cove Lily Motel. Wearing evil grins on their faces, the FireHeads commence their one on one battle with the gymleaders, and begin to attack.

Meanwhile, on the abadoned ship, Wattson and Flannery are still struggling fight down Kyogre by Manectric and Magcargo. Up in the air, Shelly and Matts, each flying on a Vibrava, secretly watch over the scene, and grunt in frustration that the gymleaders are thwarting their scheme to expand the ocean via the sea titan’s powers. Shelly remarks that they should figure out a way themselves to stop the meddlers before their leader and Sean come back from the Seafloor Cavern, and takes out her handheld dualscreen device to check on the two’s current location. To her surprise, while Archie is still underwater, Sean has returned above ground, and is moving towards their direction.

Matts grins that with the combined efforts of their SSS Trio, they will have little trouble fending off the gymleaders, and Kyogre shall unleash its full potential very soon. Just then, they notice something flying close, and decide that it must be Sean on his Pelipper. However, to their shock, it is the Fortree gymleader Winona, who quickly commands a dragonbreath from her Altaria the moment she spots the two Team Aqua admins. Shelly manages to evade narrowly, but Matts’s Vibrava gets hit head-on. The blast draws the attention of Wattson and Flannery, and the Lavaridge gymleader exclaims in exhiliration at the arrival of their supervisor while also noticing for the first time the presence of the blue-attired villains.

Winona hollers that with the Pokémon Association’s Chairman taking over her role as the central commander, she can leave all concerns behind and give her best in fighting as an independent trainer. Sending out Skarmory, she orders the steel bird to lower the foe’s special defense by metal sound, and blasts Matts’s Vibrava with Altaria’s flamethrower. She then follows up by Skarmory’s aircutter, and Flannery and Wattson watch with amazement at the young woman’s battling skills.

Shelly curses in anger, and attempts to ambush Winona from behind. Fortunately, Flannery sees this, and quickly leaps to her feet as Wattson tells her to help Winona while he deals with Kyogre alone. Popping out from its greatball, Flannery’s Vulpix stops Shelly in her tracks by firing off a will-o-wisp, and instantly burns her Vibrava. Winona thanks Flannery for her help, and the two decide to each take on one of the TA admins. On a closer look, Flannery recognizes Shelly as one of those involved in the cessation of Mt. Chimney’s volcanic activity, and swears to beat her for the unforgiveable thing she did to her town. Angered by Flannery’s attitude as well, Shelly swoops down on her Vibrava, and Flannery immediately orders flamethrowers from Magcargo and Vulpix. However, the Team Aqua admin circles keeps herself airborne on Vibrava, and adeptly avoids the attacks.

As Shelly and Matts keep Winona and Flannery occupied, Wattson is starting to have trouble holding down Kyogre by Manectric alone. He notices that the sea titan has become more ferocious than it initially was, and gets a feeling that it seems to be fighting now with a clear will which wild Pokémon usually lack. Just then, a voice comes on to compliment on Wattson for his keen observation, and remarks that their team leader, Archie, has gained possession of the legendary Blue Orb, and is indeed giving direct orders to Kyogre via the mystical jewel. Watching in disbelief, the Mauville gymleader lets out a gasp as Sean emerges from the sea with an evil grin on his face.

Back at the severely flooded Slateport City, swimmerboy Jack is surfing on his Gyarados and looking out for those who still have not evacuated to New Mauville. He is about to be convinced that the city is empty save for wild Pokémon when he suddenly spots a blind boy and his Magikarp inside a house. Hurrying over, he climbs in through the window, and hollers that everyone else has evacuated, startling the boy who immediately lets out a yelp.

Jack notices a stone plate on the desk, and the blind boy grins that he must have been too consumed in deciphering it. The swimmerboy is curious to know what the seemingly ancient item is, and the boy explains that it was unearthed during an excavation at a historical site, with a message carved in braille on it which he reads by feeling with the tip of his fingers. Amazed by what the boy can do, Jack wonders where he learnt the skill, and the boy reveals that it was taught to him by someone whom he met during a hospital stay not long ago, the same person who gave him the stone plate and called himself the Pokémon League Champion that leads the strongest trainers in Hoenn known as the Elite 4...